The recent controversy over Hillary Clinton’s use of a private email server for public business is all about secrecy. Did Clinton handle “classified,” or even “top secret,” emails with her server? And if so, was it “classified” when it arrived in Clinton’s custody or did it only become that way retroactively? But beneath the Clinton-versus-Congress war of words, national security experts are wrestling with a question that has plagued the intelligence community for decades: How secret is “top secret” really?

Long before Clinton made the decision to operate a private email server during her tenure at the top of the State Department, intelligence agencies had been guilty of “overclassification”: excessive secrecy that saturates decisions about what’s classified and tips the balance toward keeping way too many documents off-limits.

Now, as intelligence community officials pore over thousands of her unreleased emails, overclassification could become Clinton’s political problem. She’s facing attacks from lawmakers and GOP White House hopefuls for potentially mishandling secrets by allowing them to spill outside of secure channels. But some experts believe that much of the information likely presents almost no risk if disclosed and that some may not be very secret at all.

“The odds are good that any classified information in the Clinton emails should not have been classified,” said Elizabeth Goitein of the Brennan Center for Justice, a left-leaning law and policy think tank. Her reasoning? Estimates show that 50 percent to 90 percent of classified documents could be made public without risking national security.

“It is so rare that I have seen leaked or subsequently disclosed classified information where I think, ‘Yeah, I would expect some national security harm from releasing this information,’” Goitein said.

That doesn’t mean, however, that she and other information-freedom advocates are lining up behind Clinton. But to them, the email scandal isn’t really about security, it’s about the lack of transparency in a private system that until recently thwarted the ability to view Clinton’s emails under public records laws.

“It would be ironic if the upshot of the Hillary Clinton email story was a perception that she was not good enough at keeping secrets,” Goitein said.

“Clinton’s mistreatment of federal records and the intelligence community’s desire to retroactively overclassify are two distinct troubling problems,” said Nate Jones, an information-secrecy expert with the National Security Archive at George Washington University. “No politician is giving the right message: Blame Clinton for poor records practices, but don’t embrace overclassification while you do it.”

Already, the inspector general for federal intelligence agencies has concluded that two messages Clinton received had “top secret” content. The emails did not contain classification markings at the time. The ongoing review of thousands of Clinton’s emails for release under the Freedom of Information Act is likely to produce even more discoveries of information that officials now want off-limits, while several dozen of Clinton’s emails that have already been released contained redactions of information now deemed classified at some level.

But for now, and perhaps for a long while, the general public can only guess about whether overclassification is coming to play in the Clinton emails, as the actual content of classified messages in question can only be viewed by a select few.

Transparency advocates say that while the specifics of classified content may not be clear, the issue of overclassification should not be forgotten in the furor.

“It’s the conversation we are not having because we are talking about trying to track down every last scrap of classified information that might have been on the Clinton server,” said Steven Aftergood, a secrecy expert of the Federation of American Scientists. “I sort of cringe every time I read another story about the Clinton emails because it is the wrong conversation to have. We do have a problem with classification but it is not primarily a matter of safeguarding, it is a question of what is the proper scope of classification.”

Critics such as Goitein argue that intelligence agencies often abuse their classification discretion in a way that keeps information about federal policies and actions hidden from public view and could even worsen security by impeding information-sharing among agencies.

A report that Goitein co-authored in 2011 lays out several “stark” examples of secrecy with respect to information ranging from decades-old CIA budgets to parts of a 2006 diplomatic cable marked “confidential” that simply described how weddings are conducted in the Russian republic of Dagestan.

Concern about overclassification is not only the province of the Left: Shortly after the disclosures of information taken by contractor Edward Snowden began in 2013, California GOP Rep. Duncan Hunter said he feared that overclassification could jeopardize security because several million people need security clearances.

Richard Lempert, in a lengthy analysis of Clinton’s email woes published last week by the Brookings Institution, notes that “security professionals have a reputation for erring in the direction of overclassification.”

President Obama issued an executive order in 2009 aimed at part in lessening the overclassification problem. But Lempert, a former Homeland Security Department official, writes, “If … my experience within one agency was typical, some at the operational level may not have fully bought in to the president’s slant.”

There have been signs that intelligence agencies’ zeal to classify is easing, though it’s a notoriously tough problem to gauge.

A National Archives and Records Administration report this year found that in fiscal year 2014, executive-branch agencies made 46,800 “original” classification decisions, which refers to a determination that unauthorized disclosure could “reasonably be expected to cause damage to the national security.” That’s a 20 percent drop from the prior year and continues a years-long downward trend.

Far more common are so-called derivative classifications, defined as “incorporating, paraphrasing, restating, or generating in new form information that is already classified.” There were an estimated 77.52 million derivative-classification decisions in fiscal 2014, a 3 percent drop from the prior year, the report finds. Goitein and other critics note that agency guidelines for such decisions often lead to new information being placed off limits.

Aftergood says the drop in original classification decisions—that is, designations of new secrets—to the lowest level on record is good news. But that doesn’t mean overclassification doesn’t remain a major problem.

For Clinton, questions and revelations about classified information are damaging, in part because in March she said: “I did not email any classified material to anyone on my email. There is no classified material.” Clinton and her campaign have since softened the phrasing, saying that she did not send or receive any information that was marked classified at the time.

Scrutiny of Clinton’s email practices intensified this month. Charles McCullough, the federal intelligence community’s inspector general, revealed that at least two messages that crossed Clinton’s private server contained information that is “top secret”—the highest level of classification. McCullough found two others with classified information, and he reviewed just a small subset of roughly 30,000 emails that Clinton turned over to the State Department.

The four messages were not marked classified at the time, but McCullough and the State Department’s inspector general say the messages contained classified information when they were generated, and should not have crossed Clinton’s personal system.

Aftergood, while cautioning he does not know the specifics of the few emails that McCullough already flagged, is rather circumspect about the “top secret” finding. Aftergood said his “antennae shook a little” when he saw the “top secret” conclusion, noting the State Department has not endorsed McCullough’s claim.

“I don’t think the IG is fabricating or prevaricating or making stuff up. It is just not the last word on the subject, because it is possible for different officials in the same agency, and for different agencies to disagree on the status of classified information,” said Aftergood, who directs his group’s Project on Government Secrecy.

“It remains significant that there is a difference of opinion between State and the intelligence community, and that in turn reflects the subjective character of the classification system,” he said.

The questions about Clinton’s messages aren’t going away anytime soon. Ongoing vetting of Clinton’s messages could ensure that a substantial number of emails, though it’s unclear how many, will remain beyond the public’s reach, even as State has begun releasing thousands of messages in monthly batches under a court order.

On Monday, the State Department informed a federal judge that staff from intelligence agencies have, so far, flagged 305 documents for referral to their agencies for more consultation. The reviewers are aiding the State Department’s review of tens of thousands of pages of Clinton’s emails for release under the Freedom of Information Act.

Already, the review for release under FOIA has found—and redacted—63 messages with classified material in more than 3,000 messages released thus far, though State Department spokesman John Kirby said Monday that most of those were classified at a very low level.

The claim of “top secret” information has generated a fresh burst of criticism, but there are immediate doubts about the conclusion. The Associated Press, citing unnamed officials who have read the exchanges, reported late last week on the two emails labeled “top secret.” One included discussion of a drone strike, while “A second conversation could have improperly referred to highly classified material, but it also could have reflected information collected independently,” the AP reported.

Sen. Dianne Feinstein, the top Democrat on the Senate’s Intelligence Committee, has signaled skepticism about the claims of classified information in Clinton’s messages.

In a statement last week, Feinstein, who has access to the four messages that the intelligence community IG has flagged, said that none of them were written by Clinton, and added: “The questions are whether she received emails with classified information in them, and if so, whether information in those emails should have been classified in the first place. Those questions have yet to be answered.”

The State Department, meanwhile, has subtly aided Clinton by declining to support intelligence community claims of “top secret” information. Kirby said recently that they were not marked as classified and that they were circulated on unclassified systems in 2009 and 2011, and then forwarded to Clinton.

He said last week that State would work with the director of national intelligence to resolve whether the material is classified. A senior State official also indicated that what’s known as “parallel reporting” could be at play—that is, cases in which different agencies gather information from both open and sensitive sources.

“It is common for State Department employees to learn information from open sources, including press reports, that may also be independently learned through entirely separate means within the intelligence community,” the official said.

Aftergood says he can’t point the finger at overclassification when it comes to the two emails without knowing more specifics, but suggests it could be at play. “When it comes to drones, CIA has insisted on formally classifying the topic long after it became public knowledge. It is probably the biggest open secret there is,” he said.

Critics of overclassification say the amount of material needlessly kept from public view is vast. Thomas Kean, the former GOP governor of New Jersey who later chaired the commission that probed the September 11 attacks, once remarked that “three-quarters of what I read that was classified shouldn’t have been.”

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